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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.14

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-09-25, 17:26 CEST based on data in: /kyukon/scratch/gent/vo/000/gvo00027/vsc42458/JAV2201_plasmapaper/output/shortread_sequencing


        General Statistics

        Showing 390/390 rows and 13/15 columns.
        Sample Name% AssignedM Assigned% DupsFrag Length% AlignedM Aligned% AlignedM Aligned% BP Trimmed% Dups% GCMedian Read LengthM Seqs
        06_RNA026841_srout
        20.9%
        0.8
        06_RNA026842_srout
        22.4%
        0.6
        06_RNA026843_srout
        16.1%
        0.5
        06_RNA026844_srout
        17.9%
        0.4
        06_RNA026845_srout
        12.5%
        0.0
        06_RNA026846_srout
        1.0%
        0.0
        06_RNA026847_srout
        3.6%
        0.0
        06_RNA026848_srout
        1.4%
        0.0
        06_RNA026849_srout
        0.7%
        0.0
        06_RNA026850_srout
        5.0%
        0.0
        06_RNA026851_srout
        1.4%
        0.0
        06_RNA026852_srout
        4.0%
        0.0
        06_RNA026853_srout
        1.2%
        0.0
        06_RNA026854_srout
        1.8%
        0.0
        06_RNA026855_srout
        18.1%
        0.2
        06_RNA026856_srout
        9.3%
        0.1
        06_RNA026857_srout
        8.3%
        0.1
        06_RNA026858_srout
        13.2%
        0.1
        06_RNA026859_srout
        24.9%
        0.2
        06_RNA026860_srout
        8.3%
        0.2
        06_RNA026861_srout
        10.4%
        0.1
        06_RNA026862_srout
        13.7%
        0.0
        06_RNA026863_srout
        7.6%
        0.1
        06_RNA026864_srout
        13.9%
        0.3
        06_RNA026865_srout
        12.1%
        0.1
        06_RNA026866_srout
        6.6%
        0.0
        RNA026841
        58.4%
        RNA026841_1
        76.4%
        57%
        51 bp
        22.4
        RNA026841_1_cons
        54.4%
        57%
        50 bp
        3.8
        RNA026841_1_extract
        38.9%
        54.4%
        57%
        50 bp
        3.8
        RNA026841_1_trim
        75.4%
        57%
        50 bp
        19.8
        RNA026841_1_umitrim
        152.0bp
        76.5%
        2.9
        72.4%
        55%
        30 bp
        3.8
        RNA026841_2
        11.2%
        21.8%
        58%
        51 bp
        22.4
        RNA026841_2_cons
        0.9%
        58%
        50 bp
        3.8
        RNA026841_2_extract
        28.0%
        30.6%
        62%
        42 bp
        3.8
        RNA026841_2_trim
        16.0%
        58%
        50 bp
        19.8
        RNA026841_2_umitrim
        68.1%
        60%
        30 bp
        3.8
        RNA026841_PicardMarkDuplicates_htseq
        40.6%
        0.5
        RNA026841_UMItoolsDedup_htseq
        22.7%
        0.6
        RNA026841_calib_htseq
        21.1%
        0.6
        RNA026842
        56.0%
        RNA026842_1
        79.9%
        55%
        51 bp
        18.9
        RNA026842_1_cons
        53.6%
        55%
        50 bp
        2.7
        RNA026842_1_extract
        38.8%
        53.6%
        55%
        50 bp
        2.7
        RNA026842_1_trim
        79.0%
        55%
        50 bp
        16.6
        RNA026842_1_umitrim
        135.3bp
        72.8%
        2.0
        71.5%
        53%
        30 bp
        2.7
        RNA026842_2
        11.6%
        28.2%
        56%
        51 bp
        18.9
        RNA026842_2_cons
        0.7%
        57%
        50 bp
        2.7
        RNA026842_2_extract
        28.0%
        29.3%
        60%
        42 bp
        2.7
        RNA026842_2_trim
        22.4%
        56%
        50 bp
        16.6
        RNA026842_2_umitrim
        67.1%
        57%
        30 bp
        2.7
        RNA026842_PicardMarkDuplicates_htseq
        36.2%
        0.3
        RNA026842_UMItoolsDedup_htseq
        24.7%
        0.4
        RNA026842_calib_htseq
        23.6%
        0.4
        RNA026843
        60.8%
        RNA026843_1
        81.2%
        56%
        51 bp
        23.4
        RNA026843_1_cons
        56.2%
        57%
        50 bp
        3.3
        RNA026843_1_extract
        38.8%
        56.2%
        57%
        50 bp
        3.3
        RNA026843_1_trim
        80.6%
        56%
        50 bp
        21.0
        RNA026843_1_umitrim
        152.6bp
        71.1%
        2.3
        73.5%
        55%
        30 bp
        3.3
        RNA026843_2
        10.1%
        29.9%
        58%
        51 bp
        23.4
        RNA026843_2_cons
        1.1%
        58%
        50 bp
        3.3
        RNA026843_2_extract
        27.9%
        34.1%
        62%
        42 bp
        3.3
        RNA026843_2_trim
        25.1%
        57%
        50 bp
        21.0
        RNA026843_2_umitrim
        69.4%
        59%
        30 bp
        3.3
        RNA026843_PicardMarkDuplicates_htseq
        31.4%
        0.3
        RNA026843_UMItoolsDedup_htseq
        17.2%
        0.3
        RNA026843_calib_htseq
        16.1%
        0.4
        RNA026844
        61.0%
        RNA026844_1
        84.3%
        56%
        51 bp
        18.3
        RNA026844_1_cons
        56.2%
        57%
        50 bp
        2.4
        RNA026844_1_extract
        39.1%
        56.2%
        57%
        50 bp
        2.4
        RNA026844_1_trim
        84.2%
        56%
        50 bp
        16.8
        RNA026844_1_umitrim
        140.6bp
        68.4%
        1.6
        73.8%
        55%
        30 bp
        2.4
        RNA026844_2
        8.3%
        28.8%
        57%
        51 bp
        18.3
        RNA026844_2_cons
        0.6%
        58%
        50 bp
        2.4
        RNA026844_2_extract
        28.1%
        28.1%
        61%
        42 bp
        2.4
        RNA026844_2_trim
        25.4%
        57%
        50 bp
        16.8
        RNA026844_2_umitrim
        68.9%
        59%
        30 bp
        2.4
        RNA026844_PicardMarkDuplicates_htseq
        36.7%
        0.2
        RNA026844_UMItoolsDedup_htseq
        23.0%
        0.3
        RNA026844_calib_htseq
        22.2%
        0.3
        RNA026845
        23.4%
        RNA026845_1
        93.2%
        51%
        51 bp
        11.6
        RNA026845_1_cons
        20.9%
        51%
        50 bp
        0.4
        RNA026845_1_extract
        39.0%
        20.9%
        51%
        50 bp
        0.4
        RNA026845_1_trim
        93.5%
        51%
        50 bp
        11.0
        RNA026845_1_umitrim
        143.6bp
        6.2%
        0.0
        38.2%
        48%
        30 bp
        0.4
        RNA026845_2
        5.5%
        58.4%
        51%
        51 bp
        11.6
        RNA026845_2_cons
        0.7%
        52%
        50 bp
        0.4
        RNA026845_2_extract
        28.0%
        5.7%
        54%
        42 bp
        0.4
        RNA026845_2_trim
        57.3%
        51%
        50 bp
        11.0
        RNA026845_2_umitrim
        30.6%
        50%
        30 bp
        0.4
        RNA026845_PicardMarkDuplicates_htseq
        4.0%
        0.0
        RNA026845_UMItoolsDedup_htseq
        4.0%
        0.0
        RNA026845_calib_htseq
        3.9%
        0.0
        RNA026846
        26.0%
        RNA026846_1
        89.0%
        50%
        51 bp
        7.0
        RNA026846_1_cons
        25.6%
        50%
        50 bp
        0.4
        RNA026846_1_extract
        39.1%
        25.6%
        50%
        50 bp
        0.4
        RNA026846_1_trim
        88.7%
        50%
        50 bp
        6.7
        RNA026846_1_umitrim
        116.5bp
        5.1%
        0.0
        43.4%
        47%
        30 bp
        0.4
        RNA026846_2
        4.9%
        44.0%
        51%
        51 bp
        7.0
        RNA026846_2_cons
        0.3%
        52%
        50 bp
        0.4
        RNA026846_2_extract
        28.0%
        11.1%
        54%
        42 bp
        0.4
        RNA026846_2_trim
        42.7%
        51%
        50 bp
        6.7
        RNA026846_2_umitrim
        37.6%
        50%
        30 bp
        0.4
        RNA026846_PicardMarkDuplicates_htseq
        3.9%
        0.0
        RNA026846_UMItoolsDedup_htseq
        3.5%
        0.0
        RNA026846_calib_htseq
        3.6%
        0.0
        RNA026847
        13.6%
        RNA026847_1
        73.9%
        51%
        51 bp
        5.9
        RNA026847_1_cons
        19.8%
        50%
        50 bp
        0.6
        RNA026847_1_extract
        38.7%
        19.8%
        50%
        50 bp
        0.6
        RNA026847_1_trim
        72.2%
        51%
        50 bp
        5.2
        RNA026847_1_umitrim
        67.5bp
        6.8%
        0.0
        39.5%
        48%
        30 bp
        0.6
        RNA026847_2
        10.6%
        30.9%
        52%
        51 bp
        5.9
        RNA026847_2_cons
        0.1%
        52%
        50 bp
        0.6
        RNA026847_2_extract
        27.8%
        6.4%
        54%
        42 bp
        0.6
        RNA026847_2_trim
        26.2%
        52%
        50 bp
        5.2
        RNA026847_2_umitrim
        32.4%
        50%
        30 bp
        0.6
        RNA026847_PicardMarkDuplicates_htseq
        3.8%
        0.0
        RNA026847_UMItoolsDedup_htseq
        3.6%
        0.0
        RNA026847_calib_htseq
        3.6%
        0.0
        RNA026848
        27.1%
        RNA026848_1
        77.8%
        51%
        51 bp
        4.0
        RNA026848_1_cons
        33.5%
        50%
        50 bp
        0.5
        RNA026848_1_extract
        38.6%
        33.5%
        50%
        50 bp
        0.5
        RNA026848_1_trim
        76.0%
        50%
        50 bp
        3.5
        RNA026848_1_umitrim
        102.3bp
        8.8%
        0.0
        52.4%
        47%
        30 bp
        0.5
        RNA026848_2
        10.7%
        32.5%
        52%
        51 bp
        4.0
        RNA026848_2_cons
        0.1%
        52%
        50 bp
        0.5
        RNA026848_2_extract
        27.8%
        15.3%
        54%
        42 bp
        0.5
        RNA026848_2_trim
        26.8%
        52%
        50 bp
        3.5
        RNA026848_2_umitrim
        47.4%
        51%
        30 bp
        0.5
        RNA026848_PicardMarkDuplicates_htseq
        9.5%
        0.0
        RNA026848_UMItoolsDedup_htseq
        7.5%
        0.0
        RNA026848_calib_htseq
        7.5%
        0.0
        RNA026849
        20.0%
        RNA026849_1
        88.6%
        51%
        51 bp
        7.7
        RNA026849_1_cons
        19.1%
        51%
        50 bp
        0.5
        RNA026849_1_extract
        39.2%
        19.1%
        51%
        50 bp
        0.5
        RNA026849_1_trim
        88.2%
        51%
        50 bp
        7.4
        RNA026849_1_umitrim
        64.2bp
        3.9%
        0.0
        36.9%
        48%
        30 bp
        0.5
        RNA026849_2
        4.5%
        44.6%
        52%
        51 bp
        7.7
        RNA026849_2_cons
        0.3%
        52%
        50 bp
        0.5
        RNA026849_2_extract
        28.0%
        6.8%
        55%
        42 bp
        0.5
        RNA026849_2_trim
        43.4%
        52%
        50 bp
        7.4
        RNA026849_2_umitrim
        30.0%
        50%
        30 bp
        0.5
        RNA026849_PicardMarkDuplicates_htseq
        2.7%
        0.0
        RNA026849_UMItoolsDedup_htseq
        2.5%
        0.0
        RNA026849_calib_htseq
        2.5%
        0.0
        RNA026850
        21.7%
        RNA026850_1
        92.5%
        52%
        51 bp
        14.8
        RNA026850_1_cons
        28.3%
        51%
        50 bp
        0.6
        RNA026850_1_extract
        39.3%
        28.3%
        51%
        50 bp
        0.6
        RNA026850_1_trim
        92.5%
        52%
        50 bp
        14.1
        RNA026850_1_umitrim
        140.2bp
        5.5%
        0.0
        48.2%
        49%
        30 bp
        0.6
        RNA026850_2
        5.2%
        58.1%
        53%
        51 bp
        14.8
        RNA026850_2_cons
        0.7%
        53%
        50 bp
        0.6
        RNA026850_2_extract
        28.1%
        11.4%
        55%
        42 bp
        0.6
        RNA026850_2_trim
        56.6%
        52%
        50 bp
        14.1
        RNA026850_2_umitrim
        41.1%
        51%
        30 bp
        0.6
        RNA026850_PicardMarkDuplicates_htseq
        4.9%
        0.0
        RNA026850_UMItoolsDedup_htseq
        4.6%
        0.0
        RNA026850_calib_htseq
        4.7%
        0.0
        RNA026851
        27.4%
        RNA026851_1
        86.7%
        51%
        51 bp
        9.7
        RNA026851_1_cons
        28.2%
        50%
        50 bp
        0.7
        RNA026851_1_extract
        39.0%
        28.2%
        50%
        50 bp
        0.7
        RNA026851_1_trim
        86.4%
        51%
        50 bp
        9.2
        RNA026851_1_umitrim
        102.5bp
        6.2%
        0.0
        48.3%
        48%
        30 bp
        0.7
        RNA026851_2
        5.3%
        46.4%
        52%
        51 bp
        9.7
        RNA026851_2_cons
        0.4%
        53%
        50 bp
        0.7
        RNA026851_2_extract
        27.9%
        14.0%
        55%
        42 bp
        0.7
        RNA026851_2_trim
        44.8%
        52%
        50 bp
        9.2
        RNA026851_2_umitrim
        42.3%
        51%
        30 bp
        0.7
        RNA026851_PicardMarkDuplicates_htseq
        8.1%
        0.0
        RNA026851_UMItoolsDedup_htseq
        6.3%
        0.0
        RNA026851_calib_htseq
        6.4%
        0.0
        RNA026852
        23.9%
        RNA026852_1
        89.0%
        49%
        51 bp
        11.8
        RNA026852_1_cons
        29.2%
        49%
        50 bp
        0.7
        RNA026852_1_extract
        39.1%
        29.2%
        49%
        50 bp
        0.7
        RNA026852_1_trim
        88.5%
        49%
        50 bp
        11.4
        RNA026852_1_umitrim
        76.6bp
        9.6%
        0.1
        49.8%
        47%
        30 bp
        0.7
        RNA026852_2
        4.4%
        48.1%
        51%
        51 bp
        11.8
        RNA026852_2_cons
        0.5%
        52%
        50 bp
        0.7
        RNA026852_2_extract
        27.9%
        13.0%
        54%
        42 bp
        0.7
        RNA026852_2_trim
        46.6%
        51%
        50 bp
        11.4
        RNA026852_2_umitrim
        43.9%
        50%
        30 bp
        0.7
        RNA026852_PicardMarkDuplicates_htseq
        3.9%
        0.0
        RNA026852_UMItoolsDedup_htseq
        3.5%
        0.0
        RNA026852_calib_htseq
        3.5%
        0.0
        RNA026853
        29.0%
        RNA026853_1
        88.2%
        53%
        51 bp
        12.3
        RNA026853_1_cons
        33.6%
        52%
        50 bp
        1.1
        RNA026853_1_extract
        39.4%
        33.6%
        52%
        50 bp
        1.1
        RNA026853_1_trim
        87.8%
        53%
        50 bp
        11.9
        RNA026853_1_umitrim
        102.1bp
        6.0%
        0.1
        56.5%
        50%
        30 bp
        1.1
        RNA026853_2
        4.4%
        39.6%
        53%
        51 bp
        12.3
        RNA026853_2_cons
        0.2%
        54%
        50 bp
        1.1
        RNA026853_2_extract
        28.1%
        14.7%
        56%
        42 bp
        1.1
        RNA026853_2_trim
        38.0%
        53%
        50 bp
        11.9
        RNA026853_2_umitrim
        50.2%
        52%
        30 bp
        1.1
        RNA026853_PicardMarkDuplicates_htseq
        9.1%
        0.0
        RNA026853_UMItoolsDedup_htseq
        7.1%
        0.0
        RNA026853_calib_htseq
        7.2%
        0.0
        RNA026854
        34.3%
        RNA026854_1
        93.6%
        51%
        51 bp
        20.2
        RNA026854_1_cons
        23.0%
        50%
        50 bp
        0.7
        RNA026854_1_extract
        39.4%
        23.0%
        50%
        50 bp
        0.7
        RNA026854_1_trim
        93.2%
        51%
        50 bp
        19.9
        RNA026854_1_umitrim
        106.2bp
        6.7%
        0.0
        38.0%
        48%
        30 bp
        0.7
        RNA026854_2
        3.2%
        60.4%
        51%
        51 bp
        20.2
        RNA026854_2_cons
        0.8%
        52%
        50 bp
        0.7
        RNA026854_2_extract
        28.1%
        8.7%
        54%
        42 bp
        0.7
        RNA026854_2_trim
        59.5%
        51%
        50 bp
        19.9
        RNA026854_2_umitrim
        32.1%
        50%
        30 bp
        0.7
        RNA026854_PicardMarkDuplicates_htseq
        6.5%
        0.0
        RNA026854_UMItoolsDedup_htseq
        5.7%
        0.0
        RNA026854_calib_htseq
        5.7%
        0.0
        RNA026855
        70.1%
        RNA026855_1
        96.5%
        61%
        51 bp
        29.0
        RNA026855_1_cons
        69.0%
        64%
        50 bp
        1.0
        RNA026855_1_extract
        39.1%
        69.0%
        64%
        50 bp
        1.0
        RNA026855_1_trim
        96.6%
        61%
        50 bp
        28.6
        RNA026855_1_umitrim
        174.3bp
        87.7%
        0.8
        81.5%
        61%
        30 bp
        1.0
        RNA026855_2
        3.4%
        65.5%
        63%
        51 bp
        29.0
        RNA026855_2_cons
        4.1%
        65%
        50 bp
        1.0
        RNA026855_2_extract
        28.2%
        54.3%
        69%
        42 bp
        1.0
        RNA026855_2_trim
        65.4%
        62%
        50 bp
        28.6
        RNA026855_2_umitrim
        77.1%
        68%
        30 bp
        1.0
        RNA026855_PicardMarkDuplicates_htseq
        48.5%
        0.1
        RNA026855_UMItoolsDedup_htseq
        20.0%
        0.1
        RNA026855_calib_htseq
        18.3%
        0.2
        RNA026856
        68.4%
        RNA026856_1
        90.2%
        60%
        51 bp
        7.9
        RNA026856_1_cons
        54.5%
        60%
        50 bp
        0.6
        RNA026856_1_extract
        39.1%
        54.5%
        60%
        50 bp
        0.6
        RNA026856_1_trim
        90.5%
        60%
        50 bp
        7.1
        RNA026856_1_umitrim
        102.4bp
        63.9%
        0.4
        73.5%
        57%
        30 bp
        0.6
        RNA026856_2
        9.8%
        44.7%
        61%
        51 bp
        7.9
        RNA026856_2_cons
        1.3%
        60%
        50 bp
        0.6
        RNA026856_2_extract
        28.1%
        38.1%
        64%
        42 bp
        0.6
        RNA026856_2_trim
        41.0%
        61%
        50 bp
        7.1
        RNA026856_2_umitrim
        71.0%
        62%
        30 bp
        0.6
        RNA026856_PicardMarkDuplicates_htseq
        18.8%
        0.0
        RNA026856_UMItoolsDedup_htseq
        8.6%
        0.0
        RNA026856_calib_htseq
        8.1%
        0.0
        RNA026857
        58.0%
        RNA026857_1
        95.6%
        60%
        51 bp
        26.0
        RNA026857_1_cons
        39.7%
        59%
        50 bp
        0.7
        RNA026857_1_extract
        39.4%
        39.7%
        59%
        50 bp
        0.7
        RNA026857_1_trim
        95.5%
        60%
        50 bp
        25.5
        RNA026857_1_umitrim
        163.6bp
        38.9%
        0.3
        57.7%
        58%
        30 bp
        0.7
        RNA026857_2
        3.3%
        63.9%
        59%
        51 bp
        26.0
        RNA026857_2_cons
        1.5%
        60%
        50 bp
        0.7
        RNA026857_2_extract
        28.2%
        21.2%
        64%
        42 bp
        0.7
        RNA026857_2_trim
        63.4%
        59%
        50 bp
        25.5
        RNA026857_2_umitrim
        47.5%
        61%
        30 bp
        0.7
        RNA026857_PicardMarkDuplicates_htseq
        24.1%
        0.0
        RNA026857_UMItoolsDedup_htseq
        14.0%
        0.0
        RNA026857_calib_htseq
        13.9%
        0.0
        RNA026858
        73.8%
        RNA026858_1
        97.4%
        62%
        51 bp
        33.7
        RNA026858_1_cons
        70.2%
        64%
        50 bp
        0.5
        RNA026858_1_extract
        38.6%
        70.2%
        64%
        50 bp
        0.5
        RNA026858_1_trim
        97.7%
        62%
        50 bp
        33.1
        RNA026858_1_umitrim
        172.2bp
        91.2%
        0.5
        85.0%
        61%
        30 bp
        0.5
        RNA026858_2
        3.6%
        70.9%
        63%
        51 bp
        33.7
        RNA026858_2_cons
        4.5%
        65%
        50 bp
        0.5
        RNA026858_2_extract
        27.9%
        51.0%
        69%
        42 bp
        0.5
        RNA026858_2_trim
        70.8%
        63%
        50 bp
        33.1
        RNA026858_2_umitrim
        80.9%
        68%
        30 bp
        0.5
        RNA026858_PicardMarkDuplicates_htseq
        29.7%
        0.0
        RNA026858_UMItoolsDedup_htseq
        12.2%
        0.0
        RNA026858_calib_htseq
        12.3%
        0.1
        RNA026859
        33.6%
        RNA026859_1
        90.4%
        53%
        51 bp
        18.2
        RNA026859_1_cons
        32.1%
        53%
        50 bp
        0.8
        RNA026859_1_extract
        39.0%
        32.1%
        53%
        50 bp
        0.8
        RNA026859_1_trim
        90.1%
        53%
        50 bp
        17.6
        RNA026859_1_umitrim
        85.6bp
        32.1%
        0.3
        49.9%
        51%
        30 bp
        0.8
        RNA026859_2
        4.9%
        54.4%
        54%
        51 bp
        18.2
        RNA026859_2_cons
        1.0%
        54%
        50 bp
        0.8
        RNA026859_2_extract
        27.6%
        17.0%
        56%
        42 bp
        0.8
        RNA026859_2_trim
        53.2%
        54%
        50 bp
        17.6
        RNA026859_2_umitrim
        45.2%
        52%
        30 bp
        0.8
        RNA026859_PicardMarkDuplicates_htseq
        6.0%
        0.0
        RNA026859_UMItoolsDedup_htseq
        4.8%
        0.0
        RNA026859_calib_htseq
        4.7%
        0.0
        RNA026860
        76.8%
        RNA026860_1
        83.9%
        61%
        51 bp
        17.7
        RNA026860_1_cons
        64.9%
        61%
        50 bp
        2.5
        RNA026860_1_extract
        39.0%
        64.9%
        61%
        50 bp
        2.5
        RNA026860_1_trim
        83.6%
        61%
        50 bp
        15.0
        RNA026860_1_umitrim
        89.9bp
        64.7%
        1.6
        82.3%
        59%
        30 bp
        2.5
        RNA026860_2
        13.4%
        29.0%
        61%
        51 bp
        17.7
        RNA026860_2_cons
        1.4%
        62%
        50 bp
        2.5
        RNA026860_2_extract
        28.0%
        45.0%
        66%
        42 bp
        2.5
        RNA026860_2_trim
        21.6%
        61%
        50 bp
        15.0
        RNA026860_2_umitrim
        81.7%
        65%
        30 bp
        2.5
        RNA026860_PicardMarkDuplicates_htseq
        27.9%
        0.1
        RNA026860_UMItoolsDedup_htseq
        8.8%
        0.1
        RNA026860_calib_htseq
        7.8%
        0.1
        RNA026861
        61.1%
        RNA026861_1
        97.0%
        56%
        51 bp
        32.7
        RNA026861_1_cons
        47.1%
        56%
        50 bp
        0.6
        RNA026861_1_extract
        39.4%
        47.1%
        56%
        50 bp
        0.6
        RNA026861_1_trim
        96.8%
        56%
        50 bp
        32.2
        RNA026861_1_umitrim
        168.5bp
        40.7%
        0.2
        69.3%
        54%
        30 bp
        0.6
        RNA026861_2
        2.9%
        68.7%
        57%
        51 bp
        32.7
        RNA026861_2_cons
        2.0%
        58%
        50 bp
        0.6
        RNA026861_2_extract
        28.1%
        25.5%
        61%
        42 bp
        0.6
        RNA026861_2_trim
        68.0%
        57%
        50 bp
        32.2
        RNA026861_2_umitrim
        62.7%
        58%
        30 bp
        0.6
        RNA026861_PicardMarkDuplicates_htseq
        21.1%
        0.0
        RNA026861_UMItoolsDedup_htseq
        13.0%
        0.0
        RNA026861_calib_htseq
        12.8%
        0.0
        RNA026862
        66.2%
        RNA026862_1
        97.6%
        59%
        51 bp
        22.4
        RNA026862_1_cons
        58.2%
        60%
        50 bp
        0.2
        RNA026862_1_extract
        39.0%
        58.2%
        60%
        50 bp
        0.2
        RNA026862_1_trim
        97.7%
        58%
        50 bp
        22.1
        RNA026862_1_umitrim
        117.9bp
        70.2%
        0.2
        76.9%
        57%
        30 bp
        0.2
        RNA026862_2
        3.0%
        78.7%
        59%
        51 bp
        22.4
        RNA026862_2_cons
        3.4%
        61%
        50 bp
        0.2
        RNA026862_2_extract
        27.9%
        34.2%
        64%
        42 bp
        0.2
        RNA026862_2_trim
        78.3%
        59%
        50 bp
        22.1
        RNA026862_2_umitrim
        70.3%
        62%
        30 bp
        0.2
        RNA026862_PicardMarkDuplicates_htseq
        20.5%
        0.0
        RNA026862_UMItoolsDedup_htseq
        11.7%
        0.0
        RNA026862_calib_htseq
        12.0%
        0.0
        RNA026863
        68.6%
        RNA026863_1
        97.4%
        56%
        51 bp
        33.0
        RNA026863_1_cons
        79.5%
        56%
        50 bp
        1.5
        RNA026863_1_extract
        39.6%
        79.5%
        56%
        50 bp
        1.5
        RNA026863_1_trim
        97.4%
        55%
        50 bp
        32.5
        RNA026863_1_umitrim
        180.5bp
        38.1%
        0.6
        90.2%
        54%
        30 bp
        1.5
        RNA026863_2
        2.9%
        52.0%
        57%
        51 bp
        33.0
        RNA026863_2_cons
        2.6%
        58%
        50 bp
        1.5
        RNA026863_2_extract
        28.2%
        64.8%
        61%
        42 bp
        1.5
        RNA026863_2_trim
        51.1%
        56%
        50 bp
        32.5
        RNA026863_2_umitrim
        88.0%
        58%
        30 bp
        1.5
        RNA026863_PicardMarkDuplicates_htseq
        46.9%
        0.1
        RNA026863_UMItoolsDedup_htseq
        19.7%
        0.1
        RNA026863_calib_htseq
        17.7%
        0.1
        RNA026864
        78.2%
        RNA026864_1
        81.4%
        63%
        51 bp
        15.2
        RNA026864_1_cons
        66.4%
        62%
        50 bp
        2.4
        RNA026864_1_extract
        39.0%
        66.4%
        62%
        50 bp
        2.4
        RNA026864_1_trim
        80.3%
        63%
        50 bp
        13.2
        RNA026864_1_umitrim
        86.1bp
        81.1%
        2.0
        83.0%
        60%
        30 bp
        2.4
        RNA026864_2
        12.5%
        27.2%
        62%
        51 bp
        15.2
        RNA026864_2_cons
        2.3%
        62%
        50 bp
        2.4
        RNA026864_2_extract
        28.0%
        51.5%
        66%
        42 bp
        2.4
        RNA026864_2_trim
        19.3%
        62%
        50 bp
        13.2
        RNA026864_2_umitrim
        83.3%
        65%
        30 bp
        2.4
        RNA026864_PicardMarkDuplicates_htseq
        38.8%
        0.2
        RNA026864_UMItoolsDedup_htseq
        11.9%
        0.2
        RNA026864_calib_htseq
        10.2%
        0.2
        RNA026865
        67.0%
        RNA026865_1
        96.7%
        60%
        51 bp
        24.3
        RNA026865_1_cons
        61.8%
        60%
        50 bp
        0.7
        RNA026865_1_extract
        39.2%
        61.8%
        60%
        50 bp
        0.7
        RNA026865_1_trim
        96.8%
        60%
        50 bp
        23.8
        RNA026865_1_umitrim
        157.8bp
        74.1%
        0.5
        78.3%
        58%
        30 bp
        0.7
        RNA026865_2
        3.5%
        63.9%
        61%
        51 bp
        24.3
        RNA026865_2_cons
        2.9%
        62%
        50 bp
        0.7
        RNA026865_2_extract
        28.2%
        43.2%
        66%
        42 bp
        0.7
        RNA026865_2_trim
        63.5%
        61%
        50 bp
        23.8
        RNA026865_2_umitrim
        74.6%
        64%
        30 bp
        0.7
        RNA026865_PicardMarkDuplicates_htseq
        27.3%
        0.0
        RNA026865_UMItoolsDedup_htseq
        12.9%
        0.0
        RNA026865_calib_htseq
        12.3%
        0.1
        RNA026866
        58.1%
        RNA026866_1
        95.5%
        60%
        51 bp
        10.1
        RNA026866_1_cons
        49.5%
        63%
        50 bp
        0.2
        RNA026866_1_extract
        39.0%
        49.5%
        63%
        50 bp
        0.2
        RNA026866_1_trim
        96.2%
        60%
        50 bp
        9.9
        RNA026866_1_umitrim
        104.7bp
        63.6%
        0.1
        78.6%
        61%
        30 bp
        0.2
        RNA026866_2
        3.9%
        68.3%
        60%
        51 bp
        10.1
        RNA026866_2_cons
        3.9%
        62%
        50 bp
        0.2
        RNA026866_2_extract
        27.9%
        32.7%
        66%
        42 bp
        0.2
        RNA026866_2_trim
        68.0%
        59%
        50 bp
        9.9
        RNA026866_2_umitrim
        73.3%
        65%
        30 bp
        0.2
        RNA026866_PicardMarkDuplicates_htseq
        10.2%
        0.0
        RNA026866_UMItoolsDedup_htseq
        7.0%
        0.0
        RNA026866_calib_htseq
        6.7%
        0.0

        HTSeq Count

        HTSeq Count is part of the HTSeq Python package - it takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.DOI: 10.1093/bioinformatics/btu638.

        loading..

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Mark Duplicates

        Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

        The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

        To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

        • READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
        • READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
        • READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
        • READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
        • READS_UNMAPPED = UNMAPPED_READS
        loading..

        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

        XY counts

        loading..

        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

           
        loading..

        Kallisto

        Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.DOI: 10.1038/nbt.3519.

        loading..

        STAR

        STAR is an ultrafast universal RNA-seq aligner.DOI: 10.1093/bioinformatics/bts635.

        Alignment Scores

        loading..

        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.DOI: 10.14806/ej.17.1.200.

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        loading..

        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        loading..

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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